Molecular variability and genetic relationships of date palm (Phoenix dactylifera L.) cultivars based on inter-primer binding site (iPBS) markers

Abstract

Date palm (Phoenix dactylifera L.) is an important fruit crop in many arid areas and understanding the relatedness among genotypes is important for effective date palm improvement. Inter-primer binding site (iPBS) markers were used to assess the molecular variation and genetic diversity of 54 and 12 date palm (Phoenix dactylifera L.) genotypes collected from Australia and Iraq, respectively. The main objectives were to survey genetic diversity and to determine varietal differences among the collected date palm germplasm. The PCR of five iPBS primers (dominant markers) selected from an initial 60 produced a total of 111 bands ranging from 180 to 3500 bp. The PIC value for these five primers ranged from 0.2135 to 0.3289 with a mean value 0.2816. The mean expected heterozygosity (0.218), mean unbiased expected heterozygosity (0.229) and Shannon's information index (0.33) indicated a high level of inbreeding among the accessions tested. Ordination and cluster analysis showed that the genetic relationships among all accessions could be separated into geographic origin; specifically Iraqi female cultivars, exotic female cultivars collected in Australia and male accessions also collected in Australia, with a few exceptions. Date palm accessions collected in Australia and Iraq are highly divergent and the abundant genetic diversity observed provides a beginning platform for date palm improvement in Australia. The iPBS PCR-based genome fingerprinting technology used in this study is low-cost and effectively differentiated accessions of date palm and their related species.

Molecular variability and population structure of a core collection of date palm (Phoenix dactylifera L.) cultivars from Australia and the Middle East

“…Accurate identification of accessions in a germplasm collection is an important first step in crop improvement. Molecular marker systems, including SSRs, can more accurately differentiate germpalsm than methods based on morphological traits or isoenzymes because they are objective, reproducible and independent of environmental influences (Al-Najm et al, 2016;Mehmood et al, 2016). In the current study, seventeen polymorphic SSR markers discriminated a range of Phoenix dactylifera accessions including related species and provided valuable information on the genetic relationship amongst the accessions.…”

“…Our finding is similar to that of Elhoumaizi et al (2006) who showed that the Moroccan cultivar Medjool, collected from different geographical regions, had a significant range of genetic variation. These observations suggest that targeted intra-varietal selection of major date cultivars such as Medjool, Barhee and Deglet Noor could be an effective crop improvement strategy (Al-Najm et al, 2016). Date palm breeding in Iraq is highly dependent upon seed propagation and subsequent selection based on specific characteristics important to local farmers such as fruit quality and plant vigor (Khierallah et al, 2011).…”

“…Mixed pollination tends to result in variable fruit and seed size (xenia) and uneven fruit ripening caused by metaxenia (Ahmad and Ali, 1960;Shafique et al, 2011). Al-Najm et al (2016) concluded that the Australian date palm germplasm is genetically diverse for both female and male cultivars. Therefore, optimizing specific male and female cultivar combinations to increase productivity and quality should be possible and this is a significant priority for the Australian date industry.…”

“…However, analysis among closely related cultivars using morphological characters alone is often unreliable and influenced by the environment (Mehmood et al, 2013;Luo et al, 2015;Borna et al, 2016). Isozyme markers were used as an alternative, although the method was limited by the number of informative data and gave no direct assessment of DNA genomic variation (see Akbari et al 2012;Al-Najm et al, 2016;Khanam et al, 2012;Mehmood et al, 2014;Mehmood et al, 2016;Sedra et al, 1993;Sedra et al, 1996).…”

“…Restriction fragment length polymorphisms (RFLP) were used for date palm cultivar identification (Corniquel and Mercier, 1994), however the technique was considered laborious and unsuitable for studying large numbers of samples. Other molecular markers including random amplified polymorphic DNA (RAPD) (Sedra et al, 1998;Soliman et al, 2003;Williams et al, 1990), inter simple sequence repeats (ISSR) (Hamza et al, 2013;Hamza et al, 2012), amplified fragment length polymorphism (AFLP) (Al-Khalifah and Askari, 2003;Cao and Chao, 2002;El-assar et al, 2005;Elassar et al, 2003); simple sequence repeat (SSR) (Ahmed and AlQaradawi, 2009;Al-Ruqaishi et al, 2008;Elsafi, 2012;Elshibli and Korpelainen, 2008;Pintaud et al, 2010;Zehdi et al, 2004;Zehdi et al, 2012;Zehdi-Azouzi et al, 2015;Zehdi-Azouzi et al, 2016), chloroplast DNA analysis (Sakka et al, 2013;Rhouma-Chatti et al, 2014) and inter-primer binding site (iPBS) (Al-Najm et al, 2016) were used to assess the genetic diversity of date palm germplasm collected from a variety of countries. Other researchers used a combination of these marker systems to study the genetic diversity of date palm germplasm (Abdulla and Gamal, 2010;Adawy et al, 2005;Hussein et al, 2005;Saker et al, 2006;Saker et al, 2000).…”